chromomap_2: ChromoMap

In lharris421/gdexpl: Explore Genes Linked to Diseases and Diseases Linked to Genes

Description

This is a function that can be used to recreate the chromoMap from the Shiny Gadget with data outputted. This function, as noted in the genetic_disease_explore() documentation this is a function derived from the chromoMap package. This just has minor modification to make it work in this specific case.

Usage

chromomap_2(
  ch.files,
  data.files,
  title = c(),
  ch_gap = 5,
  top_margin = 25,
  left_margin = 40,
  chr_width = 6,
  chr_length = 4,
  chr_color = c("black"),
  v_align = FALSE,
  segment_annotation = FALSE,
  lg_x = 0,
  lg_y = 0,
  labels = FALSE,
  canvas_width = 500,
  canvas_height = 520,
  anno_col = c("yellow"),
  atts = NULL
)

Arguments

ch.files	filename(s) containing co-ordinates of the chromosomes to render
data.files	filename(s) containing data to annotate on the chromosomes.
title	a character string to be used as a title in plot
ch_gap	provide spacing between chromosomes.
top_margin	specify the margin from top of the plot
left_margin	specify the margin from the left of the plot
chr_width	specify the width of each chromsome
chr_length	specify the length of each chromsome.
chr_color	a vector specifying the color of each chromsome in a set. A color can be assigned to each set by passing a different color values as vector
v_align	a boolean for vertical alignment of plot
segment_annotation	a boolean to use segment-annotation algorithm
lg_x	specify the x or horizontal distance of the legend from origin(bottom right corner)
lg_y	specify the y or vertical distnce of the legend from the origin
labels	a boolean to include labels in plot
canvas_width	width of the plot
canvas_height	height of the plot
anno_col	Specifies annotation colors
atts	The atts is a file that takes a number of styling options for the chromomap. The options are canvas_height (Numeric), canvas_width (Numeric), chr_color (Character String), anno_col (Character String), chr_width (Numeric), ch_gap (Numeric), labels (T/F).

Value

A chromoMap

Examples

## Not run: 
Only run if you have the speficied files generated.

genetic_disease_explore("chromosomes.txt", "annotation.txt", readRDS("settings.rds"))


## End(Not run)

lharris421/gdexpl documentation built on Dec. 23, 2019, 6:38 p.m.